Measuring tumour dynamics via sWG sequencing of ctDNA - genelist
Alistair Martin
7 July 2017
z.caldas[caldas.genes[,order(factor(chromosome_name,levels=c(as.character(1:22),"X","Y")),as.integer(start_position))],]
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SLX-12143.D708_D506.HFMNLBBXX.s_6.sorted.dedupped SLX-12143.D708_D507.HFMNLBBXX.s_6.sorted.dedupped
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SLX-12143.D708_D508.HFMNLBBXX.s_6.sorted.dedupped SLX-12143.D709_D501.HFMNLBBXX.s_6.sorted.dedupped
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SLX-12143.D709_D502.HFMNLBBXX.s_6.sorted.dedupped SLX-12143.D709_D503.HFMNLBBXX.s_6.sorted.dedupped
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SLX-12143.D709_D504.HFMNLBBXX.s_6.sorted.dedupped SLX-12143.D709_D505.HFMNLBBXX.s_6.sorted.dedupped
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SLX-12143.D709_D506.HFMNLBBXX.s_6.sorted.dedupped SLX-12143.D709_D507.HFMNLBBXX.s_6.sorted.dedupped
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SLX-12143.D709_D508.HFMNLBBXX.s_6.sorted.dedupped SLX-12143.D710_D501.HFMNLBBXX.s_6.sorted.dedupped
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SLX-12143.D710_D502.HFMNLBBXX.s_6.sorted.dedupped SLX-12143.D710_D503.HFMNLBBXX.s_6.sorted.dedupped
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SLX-12143.D710_D504.HFMNLBBXX.s_6.sorted.dedupped SLX-12143.D710_D505.HFMNLBBXX.s_6.sorted.dedupped
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SLX-12668.D701_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D701_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D701_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D701_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D701_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D701_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D702_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D702_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D702_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D702_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D702_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D702_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D702_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D702_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D703_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D703_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D703_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D703_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D703_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D703_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D703_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D703_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D704_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D704_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D704_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D704_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D704_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D704_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D704_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D704_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D705_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D705_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D705_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D705_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D705_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D705_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D705_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D705_D508.HGHTFBBXX.s_8.sorted.dedupped
AGRN 0.460131068 -1.56657569
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SLX-12668.D706_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D706_D502.HGHTFBBXX.s_8.sorted.dedupped
AGRN -1.39538247 0.498787600
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SLX-12668.D706_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D706_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D706_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D706_D506.HGHTFBBXX.s_8.sorted.dedupped
AGRN 2.32668933 1.34923131
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SLX-12668.D706_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D706_D508.HGHTFBBXX.s_8.sorted.dedupped
AGRN 0.18401298 1.36027603
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SLX-12668.D707_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D707_D502.HGHTFBBXX.s_8.sorted.dedupped
AGRN 1.111769752 0.537444132
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SLX-12668.D707_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D707_D504.HGHTFBBXX.s_8.sorted.dedupped
AGRN 0.559533579 1.86833331
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SLX-12668.D707_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D707_D506.HGHTFBBXX.s_8.sorted.dedupped
AGRN 0.736249155 1.5038574347
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SLX-12668.D707_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D707_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D708_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D708_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D708_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D708_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D708_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D708_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D708_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D708_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D709_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D709_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D709_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D709_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D709_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D709_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D709_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D709_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D710_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D710_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D710_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D710_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D710_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D710_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D710_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D710_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D711_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D711_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D711_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D711_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D711_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D711_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D711_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D711_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D712_D501.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D712_D502.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D712_D503.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D712_D504.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D712_D505.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D712_D506.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12668.D712_D507.HGHTFBBXX.s_8.sorted.dedupped SLX-12668.D712_D508.HGHTFBBXX.s_8.sorted.dedupped
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SLX-12761.D701_D503.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D701_D504.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D701_D505.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D701_D506.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D701_D507.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D702_D502.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D702_D503.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D702_D504.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D702_D505.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D702_D506.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D702_D507.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D703_D501.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D703_D502.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D703_D503.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D703_D504.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D703_D505.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D703_D506.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D703_D507.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D703_D508.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D704_D501.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D704_D502.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D704_D503.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D704_D505.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D704_D506.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D704_D507.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D704_D508.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D705_D502.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D705_D503.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D707_D505.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D707_D506.HGJ2WBBXX.s_8.sorted.dedupped
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SLX-12761.D707_D507.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D707_D508.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 1.840721500 1.61430467
SPEN 0.330219620 -0.22030757
ARID1A -0.224271681 0.34812098
SLX-12761.D708_D501.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D708_D503.HGJ2WBBXX.s_8.sorted.dedupped
AGRN -0.32404430 0.08461047
SPEN -0.36019563 1.25979832
ARID1A -0.91364970 0.10997221
SLX-12761.D708_D504.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D708_D506.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 1.09520267 1.995347628
SPEN 3.17761847 -0.766322251
ARID1A -0.31618875 -0.583583862
SLX-12761.D708_D507.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D708_D508.HGJ2WBBXX.s_8.sorted.dedupped
AGRN -0.180462892 2.1610184803
SPEN -3.148931746 -3.0496563507
ARID1A -1.477686267 -0.2242716812
SLX-12761.D709_D501.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D709_D502.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 0.465653430 -0.22464179
SPEN -2.584866998 -1.57406297
ARID1A -1.732547232 0.52777707
SLX-12761.D709_D503.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D709_D504.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 1.067590858 0.87983056
SPEN -2.287040811 -0.33763304
ARID1A -0.792486293 0.95393803
SLX-12761.D709_D505.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D709_D506.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 0.449086345 -0.53389404
SPEN 0.343757174 -3.32943247
ARID1A -1.277139933 -3.55417643
SLX-12761.D709_D507.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D709_D508.HGJ2WBBXX.s_8.sorted.dedupped
AGRN -0.75478851 0.531921771
SPEN -4.24998613 1.011609835
ARID1A -1.93309357 0.594625848
SLX-12761.D710_D501.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D710_D502.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 1.525946882 0.86326347
SPEN 0.880746814 0.98904725
ARID1A -0.391393626 1.27564777
SLX-12761.D710_D503.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D710_D504.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 0.26132605 2.58071797
SPEN -0.73924714 -0.08944455
ARID1A 0.10997221 -0.70892532
SLX-12761.D710_D506.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D710_D507.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 1.299530051 2.20519737
SPEN 0.569383073 -1.69138844
ARID1A 1.396811183 -0.29112046
SLX-12761.D710_D508.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D711_D501.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 0.11222228 0.96818835
SPEN 1.05222250 -1.93055189
ARID1A 1.97755994 -1.17686677
SLX-12761.D711_D503.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D711_D504.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 0.70863735 2.243853906
SPEN -1.62821319 -0.852060092
ARID1A -0.13653266 -1.135086280
SLX-12761.D711_D505.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D711_D506.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 1.089680305 0.813562219
SPEN -0.603871603 -1.831276495
ARID1A -1.456796024 -0.420639966
SLX-12761.D711_D507.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D711_D508.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 0.63132428 0.752816240
SPEN 0.08654365 -2.697679948
ARID1A -1.70330089 -1.619739920
SLX-12761.D712_D501.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D712_D502.HGJ2WBBXX.s_8.sorted.dedupped
AGRN -0.412402085 1.150426284
SPEN -3.712996494 -0.378245704
ARID1A -0.240983876 -0.621186300
SLX-12761.D712_D504.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D712_D505.HGJ2WBBXX.s_8.sorted.dedupped
AGRN 0.33863911 -1.30150232
SPEN -1.15439880 -3.53249578
ARID1A -2.19631063 -0.65043264
SLX-12761.D712_D507.HGJ2WBBXX.s_8.sorted.dedupped SLX-12761.D712_D508.HGJ2WBBXX.s_8.sorted.dedupped
AGRN -0.07001566 -0.406879723
SPEN -2.95940599 -2.435953905
ARID1A -1.09330579 -2.213022823
SLX-12994.D701_D501.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D701_D502.HJM3GBBXX.s_2.sorted.dedupped
AGRN 1.65296120 -1.01986187
SPEN 2.41951545 3.08736811
ARID1A -2.36761062 1.40516728
SLX-12994.D701_D503.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D701_D504.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.14180636 -0.036881487
SPEN 0.66414595 2.031438900
ARID1A -0.68385703 1.217155092
SLX-12994.D701_D505.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D701_D506.HJM3GBBXX.s_2.sorted.dedupped
AGRN -1.15792092 0.65341373
SPEN 1.27333588 -1.37551218
ARID1A -2.42192525 0.54448926
SLX-12994.D701_D507.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D701_D508.HJM3GBBXX.s_2.sorted.dedupped
AGRN 0.09013283 -0.45658098
SPEN 0.85818422 0.76342135
ARID1A 1.08763558 -1.75343748
SLX-12994.D702_D501.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D702_D502.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.42896917 -1.88135030
SPEN 0.92587199 -6.46563246
ARID1A 0.44839415 -3.43719107
SLX-12994.D702_D503.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D702_D504.HJM3GBBXX.s_2.sorted.dedupped
AGRN 0.35520620 -1.2683681525
SPEN 0.25350681 -0.6309467110
ARID1A 1.54722093 0.5737356049
SLX-12994.D702_D505.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D702_D506.HJM3GBBXX.s_2.sorted.dedupped
AGRN -2.57164552 0.50430996
SPEN 0.61450825 2.92040494
ARID1A -1.69912284 2.62097943
SLX-12994.D702_D507.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D702_D508.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.23568651 0.178490620
SPEN 3.07834307 3.917671417
ARID1A -0.64625459 -2.630827685
SLX-12994.D703_D504.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D703_D506.HJM3GBBXX.s_2.sorted.dedupped
AGRN -4.233876400 -0.114194551
SPEN -4.123635631 -1.804201387
ARID1A -4.122391042 -1.732547232
SLX-12994.D703_D507.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D703_D508.HJM3GBBXX.s_2.sorted.dedupped
AGRN 3.4422064 2.68564284
SPEN 3.8815713 3.22725617
ARID1A -2.3550765 -2.01665454
SLX-12994.D708_D507.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D708_D508.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.169418169 0.87430820
SPEN -3.916059804 0.47913271
ARID1A -3.792325201 0.03058928
SLX-12994.D709_D501.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D709_D502.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.555983490 0.04595394
SPEN -1.880914193 -1.80871390
ARID1A -0.700569224 -1.67823260
SLX-12994.D709_D503.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D709_D504.HJM3GBBXX.s_2.sorted.dedupped
AGRN 0.21714715 0.14535645
SPEN -1.44771247 -0.69863448
ARID1A -0.12399851 -0.05714974
SLX-12994.D709_D505.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D709_D506.HJM3GBBXX.s_2.sorted.dedupped
AGRN -1.09165258 -0.484192787
SPEN 0.70927113 -2.670604840
ARID1A 0.07654782 0.519420973
SLX-12994.D709_D507.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D709_D508.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.08658274 -0.097627466
SPEN 0.61902077 -0.554233905
ARID1A -0.99303263 1.008252661
SLX-12994.D710_D501.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D710_D502.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.0368814873 -1.27389051
SPEN 0.4520576052 0.33473214
ARID1A 0.3439429309 3.39809647
SLX-12994.D710_D503.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D710_D504.HJM3GBBXX.s_2.sorted.dedupped
AGRN 0.239236599 1.64191648
SPEN -0.707659517 0.61902077
ARID1A 0.285450250 -2.26733746
SLX-12994.D710_D505.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D710_D506.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.843146299 1.55908105
SPEN -0.797909876 0.29863199
ARID1A 0.920513640 -0.04043754
SLX-12994.D710_D507.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D710_D508.HJM3GBBXX.s_2.sorted.dedupped
AGRN -2.936121394 -0.05344857
SPEN 0.298631994 0.10459372
ARID1A 0.335586834 -0.45406436
SLX-12994.D711_D502.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D711_D503.HJM3GBBXX.s_2.sorted.dedupped
AGRN -1.500307345 0.47669815
SPEN -0.166157359 -0.09395707
ARID1A 0.130862451 -0.97214238
SLX-12994.D711_D504.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D711_D505.HJM3GBBXX.s_2.sorted.dedupped
AGRN 0.7196820694 1.404454924
SPEN 0.8762342958 0.609995735
ARID1A 0.7116112093 -0.512557036
SLX-12994.D711_D507.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D711_D508.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.324044297 0.14535645
SPEN -0.486546136 -0.29702038
ARID1A 0.410791709 0.41079171
SLX-12994.D712_D501.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D712_D502.HJM3GBBXX.s_2.sorted.dedupped
AGRN -0.738221427 -0.097627466
SPEN 2.284139907 0.005318325
ARID1A -1.477686267 -0.240983876
SLX-12994.D712_D503.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D712_D504.HJM3GBBXX.s_2.sorted.dedupped
AGRN 0.316549663 -0.08658274
SPEN -1.456737502 0.28058192
ARID1A -0.211737535 -1.06823750
SLX-12994.D712_D505.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D712_D506.HJM3GBBXX.s_2.sorted.dedupped
AGRN 0.37177328 1.75236371
SPEN -1.10024858 0.52425789
ARID1A 0.45257219 0.09743806
SLX-12994.D712_D507.HJM3GBBXX.s_2.sorted.dedupped SLX-12994.D712_D508.HJM3GBBXX.s_2.sorted.dedupped
AGRN 0.045953939 0.6147571966
SPEN 1.792275447 0.6686584685
ARID1A 0.252025861 -0.9345399463
SLX-13656.D701_D501.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D701_D502.HJ777BBXX.s_8.sorted.dedupped
AGRN 0.41042981 -0.815534491
SPEN 1.29138595 -0.265432754
ARID1A 1.76447946 2.420433094
SLX-13656.D701_D503.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D701_D504.HJ777BBXX.s_8.sorted.dedupped
AGRN -2.37836286 0.77490569
SPEN -0.65802182 -0.35568311
ARID1A 1.83132824 -0.58776191
SLX-13656.D702_D507.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D702_D508.HJ777BBXX.s_8.sorted.dedupped
AGRN 1.901467479 -2.3507511
SPEN -1.912501819 9.3642806
ARID1A 1.927423357 9.3685279
SLX-13656.D703_D501.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D703_D502.HJ777BBXX.s_8.sorted.dedupped
AGRN -0.252253595 -2.091200050
SPEN -0.716684553 -1.641750740
ARID1A -1.022278967 1.472016058
SLX-13656.D703_D503.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D703_D504.HJ777BBXX.s_8.sorted.dedupped
AGRN 0.15087881 0.774905687
SPEN -0.87462268 0.406932425
ARID1A -0.42063997 -0.470776550
SLX-13656.D703_D505.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D703_D506.HJ777BBXX.s_8.sorted.dedupped
AGRN 1.906989841 0.30550494
SPEN -0.247382682 -1.28526182
ARID1A -1.147620426 -0.93036190
SLX-13656.D703_D507.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D703_D508.HJ777BBXX.s_8.sorted.dedupped
AGRN 1.33266422 0.60371247
SPEN 0.92587199 -2.29606585
ARID1A 0.20606733 -2.05007893
SLX-13656.D704_D501.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D704_D502.HJ777BBXX.s_8.sorted.dedupped
AGRN 0.349683834 -0.224641786
SPEN -4.033385271 -1.722976063
ARID1A -0.353791188 -2.350898428
SLX-13656.D704_D503.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D704_D504.HJ777BBXX.s_8.sorted.dedupped
AGRN 0.36625092 0.946098900
SPEN -1.49283765 -1.772613761
ARID1A -3.34109595 1.639138003
SLX-13656.D704_D505.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D704_D506.HJ777BBXX.s_8.sorted.dedupped
AGRN 1.178038093 0.05699866
SPEN -1.700413473 -0.77083477
ARID1A -0.094752174 0.68654292
SLX-13656.D704_D507.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D704_D508.HJ777BBXX.s_8.sorted.dedupped
AGRN 1.27744060 0.106699918
SPEN -0.36470815 1.995338756
ARID1A -1.25207164 -0.637898494
SLX-13656.D705_D501.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D705_D502.HJ777BBXX.s_8.sorted.dedupped
AGRN 2.05057125 1.730274266
SPEN -0.05334441 -0.910722826
ARID1A 0.18517708 1.726877023
SLX-13656.D705_D503.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D706_D501.HJ777BBXX.s_8.sorted.dedupped
AGRN -0.98672770 1.06759086
SPEN 0.56035804 -1.39807477
ARID1A 1.43441362 -1.51946675
SLX-13656.D706_D502.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D706_D503.HJ777BBXX.s_8.sorted.dedupped
AGRN 1.365798392 0.299982578
SPEN -0.621921675 -2.526204265
ARID1A -0.671322883 2.002628232
SLX-13656.D706_D504.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D706_D505.HJ777BBXX.s_8.sorted.dedupped
AGRN 0.63684664 -0.65538600
SPEN -0.97389808 -1.17696139
ARID1A -1.40248139 -0.68385703
SLX-13656.D706_D506.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D706_D507.HJ777BBXX.s_8.sorted.dedupped
AGRN 0.946098900 -1.411949557
SPEN -1.149886279 -1.005485704
ARID1A 0.055657576 -4.506771515
SLX-13656.D706_D508.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D707_D501.HJ777BBXX.s_8.sorted.dedupped
AGRN -1.947618645 -1.38433775
SPEN -5.089314480 -3.70848398
ARID1A -2.446993546 -2.97760572
SLX-13656.D707_D502.HJ777BBXX.s_8.sorted.dedupped SLX-13656.D707_D503.HJ777BBXX.s_8.sorted.dedupped
AGRN -1.5831427709 -1.583142771
SPEN -3.8212969260 -3.320407430
ARID1A -2.9065788940 -3.650271548
SLX-13656.D707_D504.HJ777BBXX.s_8.sorted.dedupped
AGRN -1.146876194
SPEN -3.022581243
ARID1A -1.770149670
[ reached getOption("max.print") -- omitted 103 rows ]z.score.threshold <- 3.09 #0.001
for(pat in data$meta[,sort(unique(patient))]){
i <- data$meta[,which(patient == pat & type=="plasma" & !is.na(cycle))]
i <- i[ data$meta[i,order(total.days)] ]
j <- data$meta[,which(patient == pat & type=="FFPE" & prior.post=="primary")]
i <- c(j,i)
z.cosmic.subset <- z.cosmic[,i]
colnames(z.cosmic.subset) <- data$meta[i,Sample.name]
z.cosmic.subset[which(abs(z.cosmic.subset) <= z.score.threshold,arr.ind = T)] <- 0
z.cosmic.subset[which(z.cosmic.subset < -z.score.threshold,arr.ind = T)] <- -1
z.cosmic.subset[which(z.cosmic.subset > z.score.threshold,arr.ind = T)] <- 1
#z.cosmic.subset <- z.cosmic.subset[ rowSums(abs(z.cosmic.subset) > 1.64) > 0, ]
pheatmap(z.cosmic.subset,color = c("lightskyblue","black","palevioletred"),breaks=c(-2,-.5,.5,2),legend=F,cluster_cols = F, cluster_rows = F,cellwidth = 10,cellheight = 10,gaps_col = length(j),main=paste("Patient",as.character(pat)))
}z.score.threshold <- 3.09 #0.001
for(pat in data$meta[,sort(unique(patient))]){
i <- data$meta[,which(patient == pat & type=="plasma" & !is.na(cycle))]
i <- i[ data$meta[i,order(total.days)] ]
j <- data$meta[,which(patient == pat & type=="FFPE" & prior.post=="primary")]
i <- c(j,i)
z.caldas.subset <- z.caldas[,i]
colnames(z.caldas.subset) <- data$meta[i,Sample.name]
z.caldas.subset[which(abs(z.caldas.subset) <= z.score.threshold,arr.ind = T)] <- 0
z.caldas.subset[which(z.caldas.subset < -z.score.threshold,arr.ind = T)] <- -1
z.caldas.subset[which(z.caldas.subset > z.score.threshold,arr.ind = T)] <- 1
#z.caldas.subset <- z.caldas.subset[ rowSums(abs(z.caldas.subset) > 1.64) > 0, ]
pheatmap(t(z.caldas.subset),color = c("lightskyblue","black","palevioletred"),breaks=c(-2,-.5,.5,2),legend=F,cluster_cols = F, cluster_rows = F,cellwidth = 10,cellheight = 10,gaps_row = length(j),gaps_col = caldas.genes[,which(head(chromosome_name,-1)!=tail(chromosome_name,-1))], main=paste("Patient",as.character(pat)))
}
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